[Beowulf] CCL:running GAMESS using Beowulf cluster (fwd from orbital_jc at yahoo.co.uk)

Mike Davis jmdavis at mail2.vcu.edu
Fri May 21 20:37:39 EDT 2004


I had one of the gamess linux MPI port people (Charles Castevens) 
working for me and we still had problems with the mpi version of gamess. 
We wound up using the sockets version along with a script to submit the 
jobs to pbs. For this to work you should have gamess (preferably 
installed in a common location on each node), PBS up and running (a far 
bigger task usually), modified comp files and rungms, and a script to 
handle pbs submission. I'm sorry but we never had nearly the time 
required to do a step by step guide.

I will attach a copy of the script and note the modifications:
******************
script:

#!/bin/tcsh -f
# $cwd   -- current working directory
# $0     -- program name  and path to its location
# $1     -- gamess version
# $2     -- input file name  -- w/o inp
# $3     -- nodes  (optional)
# $4    -- queue (optional)
#
set wd = $cwd
set version = $1
set name = $2
if (null$version == null ) goto usage
if (null$name == null ) goto usage
set nodes = $3
if (null$nodes == null) set nodes=1
set queue = $4
if (null$queue == null ) set queue=p2p
cat <<END >${name}.job
#!/bin/csh -f
#PBS -q $queue
#PBS -l nodes=$nodes
#alias gms       "/usr/local/gamess/seqgms"
echo "Starting GAMESS with file $name at \`date\` on \`hostname\`"
cd $wd
#printenv
/usr/u2/gamess16feb02r1/new_rungms  $name $version $nodes >& $name.log
mail $USER < ${name}.err
mv /scr/$USER/$name.dat ~/scr/$name.dat
mv /scr/$USER/$name.irc ~/scr/$name.irc
echo "GAMESS Done with status \$status at \`date\` on \`hostname\`"
END
chmod u+x ${name}.job
# submit the new script
qsub ${name}.job
#nohup ./${name}.job >& ${name}.err &
unalias rm
#rm $name.job
echo "Success!"
exit

**************************
rungms mods:

if ( `hostname` == "nameofyourcluster" ) then
 echo "creating hostlist using PBS environment PBS_NODEFILE:"
 echo $PBS_NODEFILE
 cat $PBS_NODEFILE
 set HOSTLIST='hostname'
#
# get the actual value of hostname via rsh for gamess
#
 foreach i (`cat $PBS_NODEFILE`)
  if ( $i != "hydra1.vcu.edu" )
   set HOSTLIST=($HOSTLIST `rsh $i hostname`)
  end
#
# if we are not on node001 and we are using more than 1 node
#   build a hostlist and use rsh to get the actual value returned
#   by hostname
#
  else if ( -e $PBS_NODEFILE ) then
   echo "creating hostlist using PBS environment PBS_NODEFILE:"
   cat $PBS_NODEFILE
# zero out HOSTLIST
   set HOSTLIST=''
# get the actual value of hostname via rsh for gamess
   foreach i (`cat $PBS_NODEFILE`)
    set HOSTLIST=($HOSTLIST `rsh $i hostname`)
   end
endif





Eugen Leitl wrote:

>----- Forwarded message from Jeff C <orbital_jc at yahoo.co.uk> -----
>
>From: Jeff C <orbital_jc at yahoo.co.uk>
>Date: Fri, 21 May 2004 16:12:20 +0100 (BST)
>To: CHEMISTRY at ccl.net
>Subject: CCL:running GAMESS using Beowulf cluster 
>
>Dear Comp Chem Experts,
>
>I am new to this field so I will apologize in advance
>if the following question is too trivial to the
>skilled researchers. 
>
>Currently I am trying to learn how to use gamess. The
>procedure is simple when comes to running gamess with
>single CPU. However, I am clueless when trying to run
>gamess on our newly built 16 nodes Beowulf cluster
>using MPI. I hope someone out there can give me the
>step-by-step guide.
>
>Much appreciated.
>
>Jeff Chen   
>
>
>
>	
>	
>		
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